|
| Status |
Public on Jan 13, 2021 |
| Title |
HCT116 IOX1 treatment |
| Sample type |
SRA |
| |
|
| Source name |
colorectal cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal cancer cells
treatment: IOX1
|
| Treatment protocol |
cells were treated with 10 uM of IOX1 or control for 24 hours
|
| Growth protocol |
10% FBS in DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using NucleoSpin® RNA II RNA purification kit (Machery-Nagel; #740955.20).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNAs were single-end sequenced on Illumina machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample
|
| |
|
| Submission date |
Apr 23, 2020 |
| Last update date |
Jan 13, 2021 |
| Contact name |
Jiong Li |
| E-mail(s) |
jli29@vcu.edu
|
| Phone |
3105617186
|
| Organization name |
VCU
|
| Street address |
800 E Leigh Street, suite 212
|
| City |
Richmond |
| State/province |
Virginia |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE149233 |
RNA-seq analysis of HCT116, HCP-1 and DLD-1 cells after IOX1 treatment |
|
| Relations |
| BioSample |
SAMN14681265 |
| SRA |
SRX8167069 |
